Ideally, as a means of abstracting and controlling changes between your build and deploy steps and the third party tooling. Bash scripts are either too fragile for sufficiently complex applications, and therefore unlikely to be reusable. Additionally, if the script is sufficiently complex, then you have an additional complex component that you have to maintain yourself. For many projects, this is a non-issue, but for others, it can be quite the ordeal.

Because shell scripts are more complex to write. I, myself, having used grunt and then switched to gulp, ended up favoring shell scripts / npm scripts, only to realize gets much more complex for larger projects. I think a build system abstraction is legit, and Fly is pushing the status quo to an even simpler, thinner, yet flexible alternative.

Sometimes, the hassle of allowing developers to work on it from Windows is worth the grunts.

Also, plugins. Arguably, shell scripts are also a plugin ecosystem. Perhaps a less convenient one, it's hard to say from my perspective. It's definitely hard to find versionned coffeescript bash files.

That said, wouldn't it be wonderful if Windows had bash built-in?